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1 URoL: Epigenetics
Pages 5-20

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From page 5...
... Non-coding RNAs can also play an epigenetic role. Epigenetic changes may persist throughout the lifetime of an organism, and some epigenetic changes can be transmitted to future generations.
From page 6...
... in plants, which is now in its fourth year. When plants are stressed, they establish gene expression programs through epigenetic modifications that persist into subsequent generations.
From page 7...
... In this context, Putnam and colleagues are now trying to understand how these dynamic systems successfully navigate frequent, seasonal temperature fluctuations while being extremely sensitive to longer-term temperature increases. In the process of modeling how the epigenetic state of corals depends on their environmental history, the researchers have produced new tools for predicting equilibrium states (referred to as hysteresis)
From page 8...
... Hotopp has begun to study mRNA modifications in the insect-Wolbachia system, but it is a very new area. One of her colleagues anticipates major deliverables at the end of the project in the form of "wet lab protocols … and bioinformatics pipelines for the analysis of epitranscriptomic data sets from nanopore sequencing." Probing How Epigenetic Modifications to RNA Are Recognized Many proteins are being uncovered that can write, read, or erase chemical modifications on nucleic acids in many organisms, said Lydia Contreras (The University of Texas at Austin)
From page 9...
... Since the critical thermal maximum does not vary much across elevations, bee populations from high elevations have broader thermal tolerance overall; this could be plastic, adaptive, or epigenetic, said Lozier, who is trying to tease out epigenetic correlations by analyzing DNA methylation and transcriptomics. Lozier found that bumblebees respond very quickly to cold shock at the molecular level by changing patterns of DNA methylation, which correlates with changes in metabolite production.
From page 10...
... Different Views on Adaptive or Maladaptive Epigenetic Changes A common theme considered by the PIs was whether epigenetic changes that resulted from stress, whether in the form of DNA methylation, RNA methylation, or 3D changes in chromatin architecture, were adaptive or maladaptive. Slotkin considered the persistence of rapid growth in plants following exposure to high CO2 an adaptive trait similar to the phenomenon of priming, by which a plant exposed to stress early in life is better able to handle a recurrence of the same stress later, and offered this broadly applicable rule based on his research: "The increased rate of plant growth in high CO2 is heritable; it continues even when the levels of CO2 decline.
From page 11...
... Essentially, we're able to both fast forward and rewind the adaptive clock in order to figure out how epigenetic adaptation works." This allows researchers to observe the impact of a particular epigenetic change as it plays out over many generations, potentially changing their perception of what constitutes adaptation. Human perspectives on climate change and its perturbations on temperature, CO2, and ocean acidification also influence perception, said Putnam, noting that in some cases the cell is able to buffer the impact of change.
From page 12...
... "It fundamentally comes down to a sampling problem, and sampling with a unicellular organism means if a million of them die, there's still a million left behind." As one moves across taxa, and from single cells to complex organisms, there is tremendous variation in terms of the way organisms sample the environment, the way they transduce and respond to these signals, and the way that environmental selection operates on them, said Putnam. Nonetheless, there may be clusters of taxa that employ similar epigenetic mechanisms, perhaps reflecting similar modes of sampling or selection.
From page 13...
... Transcription Regulation of Different Organisms and Cells Through Epigenetic Signals Several presenters described systems in which one cell regulates gene expression in another via epigenetic mechanisms. In C3 plants, the nurse cell responsible for nourishing the germ cell has a dynamic transcriptome, "probably a lot of RNA modifications," and it generates lots of small RNAs, said Slotkin.
From page 14...
... In their metabolic role, the algae studied by Putnam regulate production of co-factors that are essential for epigenetic modifications within their coral host; these co-factors can transmit information about the environment to the host, with algae as the messenger. Hotopp described a three-player system, where a bacterial endosymbiont regulates expression of a methyltransferase gene in the host insect, which then alters the RNA methylation profile of the virus.
From page 15...
... MULTIDISCIPLINARY RESEARCH/MULTI-TEAM RESEARCH: EXAMPLES OF CHALLENGES AND STRATEGIES FOR SUCCESS PIs described examples of the challenges posed by multidisciplinary research, such as differences in lexicon, experimental methodologies, and theoretical approaches among scientists across disciplines. PIs highlighted strategies they have employed to overcome these challenges.
From page 16...
... model, which represents the flows of energy and matter within an organism. The researchers are using the DEB model to generate a systems-level quantitative framework that can link epigenetic mechanisms to organismal and ecological performance.
From page 17...
... multiple disciplines, that standard NSF 3-year project model might be something we want to rethink." Collaborating across institutions posed bureaucratic challenges for another PI, complicating tasks like managing budgets or sharing large data sets. Multidisciplinary research "absolutely takes more time … that has to be baked into the timeframe of the grant" rather than relying on no-cost extensions, said Mulligan.
From page 18...
... "In a world where environments and ecologies are constantly under threat due to rapid climate change," wrote Putnam, "our work provides frameworks for projecting what adaptive processes might look like in single celled and multicellular organisms in this uncertain future," with the potential for "informing and providing direct conservation and restoration applications to improve reef ecosystem function for society … [such as] … to harness the inherent biological features of corals for applied approaches of stress hardening for reef restoration." One of Putnam's co-PIs
From page 19...
... Lozier's team is deploying a video game to broaden pollinator education in grades K-12, highlighting aspects of bumblebee life history, thermal stress adaptation, and threats from climate change. EDUCATION AND TRAINING Participants discussed their strategies for mentoring students and other trainees engaged in multidisciplinary research, with the goal of developing a future generation of researchers who approach scientific inquiry in a way that crosses scales and scientific disciplines.
From page 20...
... 20 Reflections on the National Science Foundation's Understanding the Rules of Life Program Other respondents noted that the nature of the project forces trainees to think beyond their own fields. As previously mentioned, working in a collaborating laboratory stimulated students' abilities to formulate questions across disciplines.


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